Analysis
Seraphina Shi
Linear regression
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 *X\] where \(Y\) is one of the epigenetic age accelerations, and \(X\) is one of the ambient exposure measurements or the urinary measurements.
The estimations of \(\beta_1\) with given \(Y\) and \(X\) are shown below, which can be interpreted as “the mean of Y changes given a one-unit increase in X while holding other variables constant”.
Ambient Exposure
## X: Ambient Exposure Measurements:## bap pm25
## Horvath EAA -0.0063 (0.0046) 0.0021 (0.0022)
## Hannum EAA -0.0022 (0.0042) -0.0002 (0.002 )
## PhenoAge EAA -0.0035 (0.0045) -0.0017 (0.0022)
## Skin&Blood EAA 0.0029 (0.0034) -0.0005 (0.0017)
## GrimAge EAA 0.0015 (0.0031) 0.001 (0.0015)
## DNAmTL 0.0001 (0.0002) 0 (0.0001)
## IEAA -0.0083* (0.0041) 0.0024 (0.002 )
## EEAA -0.0008 (0.0053) 0.0001 (0.0026)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## ANY BPE BaA
## Horvath EAA 0.0009 ***(0.0003) -0.0067 (0.0043) -0.0037 (0.0028)
## Hannum EAA 0.0004 (0.0003) -0.003 (0.004 ) -0.0014 (0.0025)
## PhenoAge EAA 0.0005 (0.0003) -0.0055 (0.0043) -0.001 (0.0027)
## Skin&Blood EAA 0.0004 (0.0002) 0.0027 (0.0032) 0.0013 (0.0021)
## GrimAge EAA 0.0006 ***(0.0002) 0.001 (0.0029) 0.0013 (0.0019)
## DNAmTL 0 (0 ) 0 (0.0002) 0 (0.0001)
## IEAA 0.0008 ** (0.0002) -0.0091* (0.0038) -0.0047 (0.0025)
## EEAA 0.0006 (0.0003) -0.0019 (0.005 ) -0.0004 (0.0032)
## <NA> <NA> <NA>
## BbF BkF CHR
## Horvath EAA -0.003 (0.0028) -0.0182 (0.0126) -0.003 (0.003 )
## Hannum EAA -0.0015 (0.0026) -0.0076 (0.0115) -0.0015 (0.0027)
## PhenoAge EAA -0.0016 (0.0028) -0.0101 (0.0124) -0.0007 (0.003 )
## Skin&Blood EAA 0.0013 (0.0021) 0.0064 (0.0094) 0.0013 (0.0022)
## GrimAge EAA 0.0013 (0.0019) 0.0055 (0.0085) 0.0019 (0.002 )
## DNAmTL 0 (0.0001) 0.0002 (0.0005) 0 (0.0001)
## IEAA -0.0041 (0.0025) -0.0236* (0.0112) -0.004 (0.0027)
## EEAA -0.0006 (0.0032) -0.0033 (0.0146) -0.0004 (0.0035)
## <NA> <NA> <NA>
## DBA FLT FLU
## Horvath EAA -0.0183 (0.0111) -0.0053 (0.0029) 0.0009 (0.0008)
## Hannum EAA -0.0091 (0.0102) -0.0025 (0.0027) -0.0003 (0.0007)
## PhenoAge EAA -0.0089 (0.0109) -0.0015 (0.0029) 0.0006 (0.0007)
## Skin&Blood EAA 0.0046 (0.0083) -0.0002 (0.0022) 0.0005 (0.0006)
## GrimAge EAA 0.0043 (0.0075) 0.001 (0.002 ) 0.0009 (0.0005)
## DNAmTL -0.0001 (0.0004) 0.0001 (0.0001) 0 (0 )
## IEAA -0.0244* (0.0098) -0.0053* (0.0026) 0.0007 (0.0007)
## EEAA -0.0054 (0.0129) -0.0024 (0.0034) -0.0001 (0.0009)
## <NA> <NA> <NA>
## IPY NAP PHE
## Horvath EAA -0.0099 (0.0078) 0.0002 ***(0.0001) 0.0007 (0.0005)
## Hannum EAA -0.0029 (0.0072) 0.0001 (0.0001) -0.0001 (0.0004)
## PhenoAge EAA -0.0091 (0.0077) 0.0001 * (0.0001) 0.0005 (0.0005)
## Skin&Blood EAA 0.0058 (0.0058) 0.0001 (0 ) 0.0003 (0.0004)
## GrimAge EAA 0.0035 (0.0053) 0.0001 ***(0 ) 0.0007 * (0.0003)
## DNAmTL 0.0001 (0.0003) 0 (0 ) 0 (0 )
## IEAA -0.0143* (0.0069) 0.0002 ** (0 ) 0.0006 (0.0004)
## EEAA -0.0014 (0.0091) 0.0001 (0.0001) 0 (0.0006)
## <NA> <NA> <NA>
## PYR
## Horvath EAA -0.0047 (0.0029)
## Hannum EAA -0.002 (0.0026)
## PhenoAge EAA -0.0013 (0.0028)
## Skin&Blood EAA 0.0003 (0.0021)
## GrimAge EAA 0.0011 (0.0019)
## DNAmTL 0.0001 (0.0001)
## IEAA -0.0049 (0.0025)
## EEAA -0.0018 (0.0033)
## <NA>Urinary Measurements
## X: Urinary Measurements:## Benzanthracene_Chrysene Naphthalene
## Horvath EAA -0.0162 (0.1265) -0.0015** (0.0006)
## Hannum EAA 0.0352 (0.1136) -0.0012* (0.0005)
## PhenoAge EAA -0.0765 (0.122 ) -0.0011 (0.0006)
## Skin&Blood EAA 0.0887 (0.0962) -0.0015***(0.0004)
## GrimAge EAA 0.1007 (0.0846) 0 (0.0004)
## DNAmTL -0.0031 (0.005 ) 0 (0 )
## IEAA -0.0706 (0.1152) -0.0011* (0.0005)
## EEAA 0.0856 (0.1441) -0.0012 (0.0006)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## 2.Methylnaphthalene 1.Methylnaphthalene Acenaphthene
## Horvath EAA -0.0068 (0.0069) -0.0099 (0.0166) 0.0385 (0.0367)
## Hannum EAA -0.0046 (0.0063) -0.021 (0.0148) 0.0341 (0.033 )
## PhenoAge EAA -0.0096 (0.0066) -0.0213 (0.0159) 0.0845 * (0.035 )
## Skin&Blood EAA -0.0071 (0.0053) -0.0243 (0.0126) -0.0146 (0.0283)
## GrimAge EAA 0.007 (0.0047) 0.0104 (0.0111) 0.0614 * (0.0241)
## DNAmTL -0.0003 (0.0003) -0.0005 (0.0007) -0.001 (0.0015)
## IEAA -0.0045 (0.0063) -0.0035 (0.015 ) 0.0604 (0.0331)
## EEAA -0.0034 (0.0079) -0.0196 (0.0189) 0.0409 (0.0419)
## <NA> <NA> <NA>
## Phenanthrene_Anthracene Fluoranthene Pyrene
## Horvath EAA 0.003 * (0.0014) 0.0369 * (0.0165) 0.4084 (0.7656)
## Hannum EAA 0 (0.0013) -0.0026 (0.0152) 0.3312 (0.693 )
## PhenoAge EAA 0.0015 (0.0014) 0.0142 (0.0164) 1.0036 (0.7185)
## Skin&Blood EAA 0.0003 (0.0011) 0.0088 (0.0129) 0.4872 (0.5667)
## GrimAge EAA 0.0029 ** (0.0009) 0.0305 ** (0.011 ) 0.7729 (0.5012)
## DNAmTL -0.0002** (0.0001) -0.0017** (0.0007) -0.013 (0.0301)
## IEAA 0.0025 (0.0013) 0.029 (0.0152) 0.7624 (0.688 )
## EEAA 0.0004 (0.0016) 0.0017 (0.0193) 0.5581 (0.8757)
## <NA> <NA> <NA>Fuel type
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(Smoky) + \beta_2 * I(Plant) + \beta_3 * I(Wood)\] where \(Y\) is one of the epigenetic age accelerations and the reference as the smokeless fuel type.
The estimations of \(\beta_0\), \(\beta_1\), \(\beta_2\), and \(\beta_3\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the smokeless fuel type to the given fuel type, while holding other variables constant”.
Childhood Exposure: Birth Fuel Type
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(Smoky) + \beta_2 * I(Wood) + \beta_3 * I(Mix)\] where \(Y\) is one of the epigenetic age accelerations and the reference as the smokeless fuel type.
The estimations of \(\beta_0\), \(\beta_1\), \(\beta_2\), and \(\beta_3\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the smokeless fuel type to the given fuel type, while holding other variables constant”.
Lifetime Exposure: Cumulative Fuel Type
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(Smoky)\] where \(Y\) is one of the epigenetic age accelerations and the reference as the mix fuel type.
The estimations of \(\beta_0\) and \(\beta_1\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the smokeless fuel type to the given fuel type, while holding other variables constant”.
Stove type
In the following section, we performed traditional linear regression with equation \[Y = \beta_0 + \beta_1 * I(HS) + \beta_2 * I(LS) + \beta_3 * I(Mix) + \beta_4 * I(PS)\] where \(Y\) is one of the epigenetic age accelerations and the baseline as the FP stove type.
The estimations of \(\beta_0\), \(\beta_1\), \(\beta_2\), \(\beta_3\), and \(\beta_4\) with given \(Y\) are shown below, which can be interpreted as “the expected change of Y if switching form the FP stove type to the given stove type, while holding other variables constant”.
Linear regression with log transformation
In the following section, we performed traditional regression with equation \[Y = \beta_0 + \beta_1 *log(x)\] where \(Y\) is one of the epigenetic age accelerations, and \(X\) is one of the ambient exposure measurements or the urinary measurements.
The estimations of \(\beta_1\) with given \(Y\) and \(log(X)\) are shown below, which can be interpreted as “the mean of Y changes given a one-unit increase in log(X) while holding other variables constant”.
Ambient Exposure
## X: Ambient Exposure Measurements:## bap pm25
## Horvath EAA -0.1362 (0.3582) 0.5568 (0.5589)
## Hannum EAA -0.2311 (0.3252) -0.2077 (0.504 )
## PhenoAge EAA -0.343 (0.3492) -0.1357 (0.5458)
## Skin&Blood EAA 0.4239 (0.2633) -0.0464 (0.431 )
## GrimAge EAA 0.1078 (0.2404) 0.3982 (0.3753)
## DNAmTL -0.0009 (0.0143) -0.0155 (0.0222)
## IEAA -0.4409 (0.3179) 0.45 (0.5099)
## EEAA -0.0792 (0.4128) -0.0484 (0.6417)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## ANY BPE BaA
## Horvath EAA 0.839 (0.4663) -0.0904 (0.3408) -0.0656 (0.2945)
## Hannum EAA 0.3086 (0.4271) -0.217 (0.3092) -0.1947 (0.2672)
## PhenoAge EAA 0.5895 (0.4442) -0.4076 (0.3313) -0.2221 (0.2874)
## Skin&Blood EAA 0.6006 (0.3401) 0.5006 * (0.249 ) 0.2773 (0.2173)
## GrimAge EAA 0.5475 (0.296 ) 0.1302 (0.2285) 0.0904 (0.1976)
## DNAmTL -0.0002 (0.0172) -0.0042 (0.0136) -0.0009 (0.0117)
## IEAA 0.6938 (0.4173) -0.3941 (0.3026) -0.3025 (0.2619)
## EEAA 0.3596 (0.5394) -0.1155 (0.3925) -0.0688 (0.3393)
## <NA> <NA> <NA>
## BbF BkF CHR
## Horvath EAA 0.0403 (0.3763) -0.1195 (0.3712) 0.0323 (0.3002)
## Hannum EAA -0.0818 (0.342 ) -0.2105 (0.3371) -0.128 (0.2727)
## PhenoAge EAA -0.2943 (0.3671) -0.2856 (0.3623) -0.2322 (0.2929)
## Skin&Blood EAA 0.4103 (0.2769) 0.4104 (0.2732) 0.1986 (0.2222)
## GrimAge EAA 0.0887 (0.2525) 0.1327 (0.249 ) 0.0771 (0.2014)
## DNAmTL -0.0004 (0.015 ) 0.0008 (0.0148) 0 (0.0119)
## IEAA -0.2556 (0.3356) -0.4337 (0.3296) -0.2023 (0.2678)
## EEAA 0.0438 (0.4335) -0.0435 (0.4278) -0.0095 (0.3459)
## <NA> <NA> <NA>
## DBA FLT FLU
## Horvath EAA -0.2082 (0.301 ) -0.1165 (0.2265) 0.9046 (0.5224)
## Hannum EAA -0.188 (0.2736) -0.2037 (0.2053) 0.1097 (0.4791)
## PhenoAge EAA -0.1554 (0.2946) -0.1963 (0.221 ) 0.425 (0.4999)
## Skin&Blood EAA 0.2699 (0.2226) 0.1118 (0.168 ) 0.5274 (0.3831)
## GrimAge EAA 0.116 (0.2022) 0.0597 (0.1521) 0.4849 (0.3336)
## DNAmTL -0.0105 (0.012 ) 0.0027 (0.009 ) -0.0073 (0.0192)
## IEAA -0.4658 (0.2663) -0.2445 (0.2015) 0.7045 (0.4681)
## EEAA -0.0709 (0.3474) -0.1096 (0.261 ) 0.1407 (0.6048)
## <NA> <NA> <NA>
## IPY NAP PHE
## Horvath EAA -0.2572 (0.3784) 1.3658 * (0.5334) 0.9223 (0.4917)
## Hannum EAA -0.31 (0.3435) 0.6014 (0.4947) 0.1548 (0.452 )
## PhenoAge EAA -0.3773 (0.3692) 0.9077 (0.5135) 0.5547 (0.4701)
## Skin&Blood EAA 0.4216 (0.2789) 0.9078 * (0.3912) 0.5075 (0.3615)
## GrimAge EAA 0.1161 (0.2542) 0.7946 * (0.341 ) 0.5432 (0.3133)
## DNAmTL -0.0037 (0.0151) -0.0073 (0.02 ) -0.0058 (0.0181)
## IEAA -0.5545 (0.3351) 1.1099 * (0.4791) 0.7783 (0.4397)
## EEAA -0.2198 (0.4362) 0.7784 (0.6243) 0.2102 (0.5706)
## <NA> <NA> <NA>
## PYR
## Horvath EAA -0.105 (0.2283)
## Hannum EAA -0.1869 (0.207 )
## PhenoAge EAA -0.2032 (0.2227)
## Skin&Blood EAA 0.1428 (0.1692)
## GrimAge EAA 0.0455 (0.1533)
## DNAmTL 0.0015 (0.0091)
## IEAA -0.254 (0.203 )
## EEAA -0.0833 (0.2631)
## <NA>Urinary Measurements
## X: Urine Measurements:## Benzanthracene_Chrysene Naphthalene
## Horvath EAA 0.2936 (0.4004) -0.099 (0.4973)
## Hannum EAA 0.0618 (0.3605) -0.0471 (0.447 )
## PhenoAge EAA -0.2225 (0.3871) -0.1788 (0.4836)
## Skin&Blood EAA 0.1819 (0.3059) -0.2704 (0.3813)
## GrimAge EAA 0.3571 (0.2679) 0.4907 (0.3313)
## DNAmTL -0.0202 (0.0157) -0.0148 (0.0197)
## IEAA -0.1899 (0.3657) 0.1153 (0.4532)
## EEAA 0.2803 (0.4572) 0.0566 (0.5687)
## [P<0.001: ***; P<0.01: **; P<0.05: *] <NA>
## 2.Methylnaphthalene 1.Methylnaphthalene Acenaphthene
## Horvath EAA 0.2761 (0.4882) 0.1266 (0.4585) 0.3522 (0.411 )
## Hannum EAA 0.3532 (0.4424) 0.0915 (0.4107) 0.377 (0.3689)
## PhenoAge EAA -0.0442 (0.4722) -0.1355 (0.4417) 0.8679 * (0.3936)
## Skin&Blood EAA -0.1176 (0.3798) -0.2415 (0.3515) -0.1501 (0.3164)
## GrimAge EAA 0.6975 * (0.3304) 0.2879 (0.307 ) 0.5668 * (0.2723)
## DNAmTL -0.0337 (0.019 ) -0.0093 (0.0181) -0.0093 (0.0163)
## IEAA 0.1716 (0.447 ) -0.0176 (0.4152) 0.4444 (0.3736)
## EEAA 0.553 (0.5545) 0.3327 (0.523 ) 0.5495 (0.4688)
## <NA> <NA> <NA>
## Phenanthrene_Anthracene Fluoranthene Pyrene
## Horvath EAA 0.8296 * (0.3619) 0.7071 (0.4384) 0.5393 (0.7146)
## Hannum EAA 0.2536 (0.3311) 0.0125 (0.398 ) 0.0884 (0.6483)
## PhenoAge EAA 0.5023 (0.3565) 0.4379 (0.4291) 0.3926 (0.6764)
## Skin&Blood EAA 0.1704 (0.2833) 0.0058 (0.3402) 0.711 (0.5271)
## GrimAge EAA 0.5306 * (0.2436) 0.5115 (0.294 ) 0.4075 (0.4719)
## DNAmTL -0.04 ** (0.0142) -0.0291 (0.0174) -0.0135 (0.0281)
## IEAA 0.5085 (0.3336) 0.4288 (0.4019) 0.7286 (0.6429)
## EEAA 0.4758 (0.4202) 0.0717 (0.5064) 0.3025 (0.8194)
## <NA> <NA> <NA>